The former commander of the USS Cole, the American war ship that was struck by a suicide boat in Yemeni waters more than eight years ago, on Thursday slammed President Barack Obama's orders to close the Guantánamo detention centre and reassess the prisoners being held there.

"We shouldn't make policy decisions based on human rights and legal advocacy groups," retired US navy Commander Kurt Lippold said in a telephone interview.

"We should consider what is best for the American people, which is not to jeopardise those who are fighting the war on terror - or even more adversely impact the families who have already suffered losses as a result of the war."

Lippold was responding to the decision by a US military judge in Guantánamo to reject a request by Pentagon lawyers to delay next week's scheduled arraignment of Abd el-Rahim al-Nashiri, a Saudi Arabian who is charged with helping orchestrate the October 2000 suicide bombing of the Cole. The bombing killed 17 US sailors.

In his ruling, the judge, US army Colonel James Pohl, said a delay in Nashiri's arraignment would deny the public's interest in a speedy trial. He also said nothing that took place at the arraignment would prevent the Obama administration from deciding to deal with Nashiri in a forum other than the military commission now set to hear his case.

Soon after becoming president, Obama ordered the Pentagon to request delays in all trials pending at Guantánamo for 120 days so that his administration could study the cases against each of the 250 or so men held as suspected terrorists and decide how to proceed in each case. Obama and his appointee to be the Pentagon's top legal officer have said they favour trials in civilian courts for terrorism suspects, if possible.

Other military judges granted the delay, including in the case of five men charged with plotting the September 11 2001 terror attacks that killed nearly 3,000 people. Family members of the 9/11 victims who were in Guantánamo to witness proceedings in that case expressed outrage at the decision.

Yesterday, Lippold called Pohl's decision "a victory for the 17 families of the sailors who lost their lives on the USS Cole over eight years ago."

The decision, however, stunned officials at the US department of defence and White House, which had just begun to grapple with Obama's order to freeze the war court and empty the detention centre within a year.

"The Department of Defence is currently reviewing Judge Pohl's ruling," said US navy Commander Jeffrey Gordon. "We will be in compliance with the president's orders regarding Guantánamo."

Nashiri's Pentagon-appointed defence lawyer, US navy Lieutenant Commander Stephen Reyes, said the prosecutor could still dismiss the charges against his client to comply with the president's request for a freeze. The charges could later be reinstated.

"The only way they can give effect to the president's order is by dismissing the charges," Reyes said.

But Lippold also denounced suggestions that the Pentagon official who oversees the Guantánamo legal cases, Susan J Crawford, could withdraw the charges, without prejudice, which would allow them to be reinstituted later, should the administration want.

Nashiri's case could prove a particularly difficult one for the Obama administration. First turned over to the CIA in 2002, he was held until late 2006 in secret detention by the CIA, which has acknowledged that it subjected him to waterboarding during that time. Obama's attorney general-designate, Eric Holder, told Congress during his confirmation hearings that he considers waterboarding torture, which is illegal under US and international law.

Nashiri told a military board reviewing his status as an enemy combatant in 2007 that he had confessed to involvement in the Cole attack only because he'd been tortured.

Under the current military commission structure, such a confession might be admissible, but it would not be in a civilian or regular military court-martial.

Lippold's own pronouncements in the case were ironic. A US navy inquiry questioned whether Lippold had taken appropriate measures to prevent an attack on the vessel. No one was in the ship's command centre when the suicide boat rammed into the Cole's side and no planning had been undertaken for such an eventuality. But Lippold was not disciplined.

Pohl's decision to go forward with the Nashiri case was denounced by the head of the American Civil Liberties Union, which said the ruling smacked of Bush administration holdovers at the Pentagon trying to prevent President Barack Obama from fulfilling his promise to close Guantánamo.

The order, said ACLU executive director Anthony Romero, "raises serious questions about whether Secretary of Defence [Robert] Gates is the 'New Gates' or is the same old Gates under a new president. Gates certainly has the power to put a halt to these proceedings, and his lack of action demonstrates that we may have more of the same - rather than the change we were promised."

Because the Pentagon sought military execution for Nashiri, the American Civil Liberties Union hired death penalty specialists to assist in his defence.